Homeobox protein NANOG (Nanog) is a 305-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q80Z64.
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The mean pLDDT of this model is 56.6 (low overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 17% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 24% |
| Below 50 | Very low: often disordered regions | 55% |
What pLDDT means and how to read it
Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal (PubMed:25825768). Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3'. Binds to the POU5F1/OCT4 promoter (By similarity). Able to autorepress…
Interacts with SMAD1 (PubMed:16801560). Interacts with SALL4 (PubMed:16840789). Interacts with ZNF281/ZFP281 (PubMed:21915945, PubMed:22988117). Interacts with PCGF1 (By similarity). Interacts with ESRRB; reciprocally modulates their transcriptional activities (PubMed:18957414). Interacts with NSD2 (PubMed:19483677)
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8YDD | X-ray | 2.5 Å | D/E=96-155 |
| 2VI6 | X-ray | 2.6 Å | A/B/C/D/E/F/G/H=96-155 |
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